PMID: 8604341Mar 15, 1996Paper

Conformational flexibility in RNA: the role of dihydrouridine

Nucleic Acids Research
J J DallugeD R Davis

Abstract

In order to further understand the structural role of the modified nucleoside dihydrouridine in RNA the solution conformations of Dp and ApDpA were analyzed by one- and two-dimensional proton NRM spectroscopy and compared with those of the related uridine-containing compounds. The analyses indicate that dihydrouridine significantly destabilizes the C3'-endo sugar conformation associated with base stacked, ordered, A-type helical RNA. Equilibrium constants (Keq = [C2'-endo]/[C3'-endo]) for C2'-endo-C3'-endo interconversion at 25 degrees C for Dp, the 5'-terminal A of ApDpA and D in ApDpA are 2.08, 1.35 and 10.8 respectively. Stabilization of the C2'-endo form was shown to be enhanced at low temperature, indicating that C2'-endo is the thermodynamically favored conformation for dihydrouridine. DeltaH values show that for Dp the C2'-endo sugar conformation is stabilized by 1.5 kcal/mol compared with Up. This effect is amplified for D in the oligonucleotide ApDpA and propagated to the 5'-neighboring A, with stabilization of the C2'-endo form by 5.3 kcal/mol for D and 3.6 kcal/mol for the 5'-terminal A. Post-transcriptional formation of dihydrouridine therefore represents a biological strategy opposite in effect to ribose methylatio...Continue Reading

References

Nov 28, 1979·Biochemical and Biophysical Research Communications·K WatanabeT Miyazawa
Nov 19, 1976·Science·G J Quigley, A Rich
Dec 25, 1976·Journal of Molecular Biology·A JackA Klug
Jul 11, 1989·Biochemistry·K B HallA G Redfield
Jan 1, 1987·Annual Review of Biochemistry·G R BjörkP M Wikström
Jul 5, 1985·Journal of Molecular Biology·E WesthofD Moras
Jun 25, 1994·Nucleic Acids Research·P A LimbachJ A McCloskey
Jul 28, 1995·The Journal of Biological Chemistry·J A KowalakJ A McCloskey
Dec 25, 1995·Nucleic Acids Research·D R Davis

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Citations

Apr 5, 2014·Journal of Chemical Information and Modeling·Indrajit DebAnsuman Lahiri
Jan 14, 2009·The Journal of Biological Chemistry·Lance W RiderBruce A Palfey
Jun 4, 2011·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Futao YuMin Yao
Mar 19, 2013·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Susan P Russell, Patrick A Limbach
Jun 11, 2011·International Journal for Quality in Health Care : Journal of the International Society for Quality in Health Care·Joris MichielsenHerman Meulemans
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·R C MorrisM S Elliott
Sep 8, 2011·Briefings in Bioinformatics·Magdalena RotherJanusz M Bujnicki
May 25, 2010·Nucleic Acids Research·Hilda David-EdenYael Mandel-Gutfreund
Nov 3, 2004·Nature Reviews. Molecular Cell Biology·Renée SchroederKatharina Semrad
Oct 12, 2014·FEBS Letters·Chen GuPeter C Dedon
Nov 26, 2009·FEBS Letters·Eric M Phizicky, Juan D Alfonzo
Sep 12, 2006·FEBS Letters·Dan F SavageAnthony C Bishop
Feb 4, 2016·Journal of Computational Chemistry·You XuLennart Nilsson
Apr 23, 2015·Proceedings of the National Academy of Sciences of the United States of America·Robert T ByrneAlfred A Antson
Dec 15, 2015·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Yuichiro NomuraTakashi Yokogawa
Oct 3, 2015·Nucleic Acids Research·Charles Bou-NaderDjemel Hamdane
May 2, 2015·RNA Biology·Efrat Kligun, Yael Mandel-Gutfreund
Apr 5, 2016·Biomolecules·Jinwei Zhang, Adrian R Ferré-DAmaré
May 12, 2015·Wiley Interdisciplinary Reviews. RNA·Jinwei Zhang, Adrian R Ferré-D'Amaré
Apr 29, 2015·Wiley Interdisciplinary Reviews. RNA·Jeremy E Wilusz
Jul 7, 2015·Acta Crystallographica. Section D, Biological Crystallography·Fiona WhelanAlfred A Antson
May 29, 2015·Journal of Inherited Metabolic Disease·Lindsey Van HauteMichal Minczuk
Apr 27, 2013·RNA Biology·Efrat Kligun, Yael Mandel-Gutfreund
Mar 31, 2015·Organic & Biomolecular Chemistry·N DyubankovaE Lescrinier
Mar 17, 2015·Nature Structural & Molecular Biology·Jonas NoeskeJamie H D Cate
Jun 30, 2012·BMC Bioinformatics·Joanna M KasprzakJanusz M Bujnicki
Nov 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Futao YuIsao Tanaka
Apr 5, 2017·Biomolecules·Christian LorenzMario Mörl
Jun 20, 2017·Archives of Biochemistry and Biophysics·Murielle Lombard, Djemel Hamdane
Jul 31, 2013·Nature·Jinwei Zhang, Adrian R Ferré-D'Amaré
Oct 3, 2014·BMC Bioinformatics·Bharat Panwar, Gajendra P S Raghava

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